+Open data
-Basic information
Entry | Database: PDB / ID: 4ml5 | ||||||
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Title | one minute iron loaded frog M ferritin mutant H54Q | ||||||
Components | Ferritin, middle subunit | ||||||
Keywords | OXIDOREDUCTASE / one minute iron soaking / four helix bundle / ferroxidase | ||||||
Function / homology | Function and homology information ferroxidase / ferroxidase activity / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasm Similarity search - Function | ||||||
Biological species | Rana catesbeiana (American bullfrog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å | ||||||
Authors | Mangani, S. / Di Pisa, F. / Pozzi, C. / Turano, P. / Lalli, D. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Time-lapse anomalous X-ray diffraction shows how Fe(2+) substrate ions move through ferritin protein nanocages to oxidoreductase sites. Authors: Pozzi, C. / Di Pisa, F. / Lalli, D. / Rosa, C. / Theil, E. / Turano, P. / Mangani, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ml5.cif.gz | 107.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ml5.ent.gz | 82.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ml5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/4ml5 ftp://data.pdbj.org/pub/pdb/validation_reports/ml/4ml5 | HTTPS FTP |
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-Related structure data
Related structure data | 4lpjC 4lqhC 4lqjC 4lqvC 4lyuC 4lyxC 4mjyC 4mkuC 4mn9C 4my7C 6i36C 3ka3S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20613.162 Da / Num. of mol.: 1 / Mutation: H54Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rana catesbeiana (American bullfrog) / Production host: Escherichia coli (E. coli) / References: UniProt: P07798, ferroxidase | ||||||
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#2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.07 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 1.6-2M magnesium chloride, 0.1M bicine, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.22→22.51 Å / Num. all: 1071136 / Num. obs: 79449 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 13.5 % / Biso Wilson estimate: 8.162 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 17.9 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3KA3 Resolution: 1.22→21.71 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.731 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.031 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.357 Å2
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Refinement step | Cycle: LAST / Resolution: 1.22→21.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.22→1.252 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 20
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